Rare micrometeorite and debris damage to craft and maybe kerbals. I didn't see this mentioned yet (but there are so many now)..

[darthgently]

There could be rare but possible micrometeorite/debris damage to craft.  Any damage would appear as a report in messages so it wouldn't sneak up on the player.  Maybe settings could limit it to active craft only, or even possible to craft on rails.  Damage could be repaired with repair kits. 

I'm imagining this as a very rare occurence, perhaps slightly less rare if in a high asteroid count area (Dres orbit) on the theory that many asteroids close together would eventually collide and create debris now and then. 

Also perhaps a higher chance when in orbit around a body with a lot of player debris floating around that hasn't been cleaned up.  Finally, leaving service bay doors open would expose the equipment inside getting damaged, but typically only parts composing the outside layer of the collision mesh could get strike damage (PVs, tanks, antennas, science instruments outside of closed service bays, etc).

For the purposes of simplicity any Kerbal inside a craft or items in inventory would be immune to this rare damage.  But woe unto the Kerbal who spends too many orbits around the Sun in a command chair.  He's toast eventually as the odds are not in his favor. 

I'm not picturing this as a major game challenge but more as a tedium breaker that adds some grit to the game.  Like maybe even a damaged tank would lose a tiny fraction of fuel over time until repaired, but the fraction would not typically be mission threatening.   And an engineer with enough experience could roll the dice to temporarily solve the issue without a repair kit even, but might have to repeat this until a repair kit is applied (add Duct Tape as default Sr. Engineer inventory item?)

On the other hand, maybe the "challenge level" of damage would best be left as a user setting.  Dialed up to the highest setting a player could get a message once in a blue moon that an entire craft and crew went down from an meteorite strike.  Ouch.

[Bej Kerman]

All damage to the vessel should be due to player incompetence. No RNG.